It comes just over a month after he was released from prison, where he was serving 25 years for human rights abuses and corruption.
The 79-year-old was given a pardon on health grounds but the court in the capital Lima says this does not apply to the new case.
He says he is innocent and will appeal against the court’s ruling.
The court also wants to try 22 others for the death-squad killings.
When current President Pedro Pablo Kuczynski granted the pardon in December, there were street protests in the capital, Lima.
Fujimori is a deeply divisive figure in Peru, respected by some and reviled by others for his government’s crackdown on two violent insurgencies during his tenure from 1990-2000.
He has low blood pressure and an irregular heartbeat.
In December, President Kuczynski’s office said he had decided to grant him a “humanitarian pardon”.
Doctors, it added, had “determined that Mr Fujimori suffers from a progressive, degenerative and incurable illness and that prison conditions represent a grave risk to his life”.
Mr Kuczynski later said: “I am convinced that those of us who consider ourselves democrats cannot allow Alberto Fujimori to die in prison. Justice is not vengeance. All pardons are by nature controversial.”
Mr Kuczynski denies pardoning Fujimori as part of a deal with his party last year to avoid his own impeachment, for allegedly receiving illegal payments from the Brazilian construction giant Odebrecht.
In 2007, he was sentenced to six years in jail for bribery and abuse of power, but two years later was sentenced to another 25 years in prison for human rights abuses committed during his time in office.
He was found him guilty of authorising other killings carried out by death squads.
An estimated 69,000 people died in the conflict between left-wing insurgents and Fujimori’s authoritarian government. (Courtesy BBC)